wenda_gpu: fast domain adaptation for genomic data

Abstract

AbstractMotivationDomain adaptation allows for the development of predictive models even in cases with limited sample data. Weighted elastic net domain adaptation specifically leverages features of genomic data to maximize transferability but the method is too computationally demanding to apply to many genome-sized datasets.ResultsWe developed wenda_gpu, which uses GPyTorch to train models on genomic data within hours on a single GPU-enabled machine. We show that wenda_gpu returns comparable results to the original wenda implementation, and that it can be used for improved prediction of cancer mutation status on small sample sizes than regular elastic net.Availability and implementationwenda_gpu is available on GitHub at https://github.com/greenelab/wenda_gpu/.Supplementary informationSupplementary data are available at Bioinformatics online.